Can change over time (months or years)
| Freeze d. | GENCODE | Release d. | Genome v. | UCSC version |
|---|---|---|---|---|
| 5.2018 | 29 | 10.2018 | GRCh38 | 29 (GRCh38) |
| 6.2014 | 21 | 10.2014 | GRCh38 | - |
| 7.2013 | 19 | 12.2013 | GRCh37 | 19 (GRCh37) |
| 7.2011 | 10 | 12.2011 | GRCh37 | 10 |
| 12.2010 | 7 | 4.2011 | GRCh37 | 7 |
| 7.2009 | 3c | 9.2009 | NCBI36/GRCh37 | 3c (NCBI36) |
You can even build your own reference genome(s)
Your lab can generate data over time
and
you must re-analyze it multiple times or combining it in many ways
They transform data
Each transformation has an input and an output
The output of the previous transformation is the input for the next one
There are many tools for many purposes and our duty is to combine them in a proper way
Linux
Its core code can be inspected and you can contribute !
It is a very very stable system
Our cluster uptime is about Years
| Source | Date | Unix | Windows | Unkw |
|---|---|---|---|---|
| W3Tech | Feb 15 | 36.85 | 32.3 | 30.5 |
| W3Tech | Feb 19 | 69.3 | 30.7 | 0 |
You can install Linux main OS or access a remote machine by network
Most of the time you share resources with others
Most of the time you share resources with others
Whatever action you are doing through a computer you are going to use a software somewhere
In any case we have 2 best friends:
The winner is ?
You can instruct the machine to do whatever you want using the keyboard typing commands.
With the terminal you can even write documents, text files.
NOT WORD FILES!!!
It is a shell which interprets your commands and acts appropriately
It is a shell which interprets your command and act appropriately
ls -la
ls -l /root
Write a file called “myfile.txt” with gedit and read it with the terminal
cat myfile.txt
Copy a file
cp myfile.txt myfile.backup.txt
now do a ls
Move a file aka Rename
mv myfile.txt MyFile.txt
now do a ls
Connect to your own machine
ssh user@localhost
if you get a message like this:
The authenticity of host 'localhost (::1)' can't be established.
ECDSA key fingerprint is SHA256:Zf595J6gKYjVYVD3R/E1AnQmsLu7QB+Ff1kmBn7vdKo.
Are you sure you want to continue connecting (yes/no)?
Type yes
Connect to a server
ssh user@192.168.200.213
now list all the connected users
who
There are many users all w/the same name
Using applications
STAR --help
The functionalities of a computer can be extended installing software
apt-get install neadd-apt-repository ppa:user/ppa-name
~/.bashrc)$PATH (e.g. shebang)On our system is already installed by the procedure is quite easy if you start from scratch.
You can start creating a conda environemnt.
A conda environment let’s you install and use software softly separated by the original system
conda create -n unimiPhD
Then you are ready to install the application for RNA-seq
conda install -y -c bioconda \
fastqc=0.11.8 \
trimmomatic=0.38 \
samtools=1.9 \
star=2.6.1b